As I understand it, a lead SNP captures the variance for all unmeasured SNPs in a region due to it's low p-value and high linkage disequilibrium. However, in different papers the region size differs (e.g. from 500kb +/- to 1mb +/-), how are these sizes chosen and why do they differ?

Edit to add examples: Xia et al. Transl Psychiatry. 2017 Aug "Genome-wide association analysis identifies common variants influencing infant brain volumes" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5611727/ -500kb region

Polushina et al. Transl Psychiatry. 2017 Dec "Analysis of the joint effect of SNPs to identify independent loci and allelic heterogeneity in schizophrenia GWAS data" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5802566/ -1mb region

  • $\begingroup$ It would be great to reference papers which use the different sizes. Otherwise it's hard to say why they chose the sizes they did. Thanks! $\endgroup$ – rotaredom Apr 26 '19 at 14:26
  • $\begingroup$ Thank you for your response, added some papers I have been looking at now, is it likely to depend on the disease being looked at? As in, the more complex and heterogenous the wider the region you might look in? Or does it depend how many SNPs pop up how big you set your boundaries? Do researchers risk a loss of information with however they set these regions? $\endgroup$ – DN1 Apr 26 '19 at 14:32

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